Downloadpathwaysforexternalreferenceslistxreflist00output_path00file_type00written_filescreatePathoutput_path0xref0path_name00net.sf.taverna.t2.activitiesbeanshell-activity0.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true output_path 0 'text/plain' java.lang.String true xref 0 'text/plain' 0 path_name 0 'text/plain' net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateFileNamepathway_name0pathway_species0path_name0file_name00net.sf.taverna.t2.activitiesbeanshell-activity0.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true pathway_name 0 'text/plain' java.lang.String true path_name 0 'text/plain' java.lang.String true pathway_species 0 'text/plain' 0 file_name 0 'text/plain' net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokecountlist1count00net.sf.taverna.t2.activitiesbeanshell-activity0.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true list 1 l('text/plain') 0 count 0 'text/plain' net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesplitLinesstring0regex0split11net.sf.taverna.t2.activitieslocalworker-activity0.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow java.lang.String true string 0 'text/plain' java.lang.String true regex 0 'text/plain' 1 split 1 l('text/plain') net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokereadXrefListfileurl0filecontents00net.sf.taverna.t2.activitieslocalworker-activity0.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow java.lang.String true fileurl 0 'text/plain' 0 filecontents 0 'text/plain' net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeclone_listcopy_number0input0clones11net.sf.taverna.t2.activitiesdataflow-activity0.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokefind_pathways_by_xrefsystem_code0identifier0pathway_ids11pathway_names11pathway_species11net.sf.taverna.t2.activitiesdataflow-activity0.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokewrite_pathwayfile_type0file_name0pathway_id0revision0writtenFile00net.sf.taverna.t2.activitiesdataflow-activity0.4net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesplitLines_regex_defaultValuevalue00net.sf.taverna.t2.activitiesstringconstant-activity0.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity \n net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokefind_pathways_by_xref_system_code_defaultValuevalue00net.sf.taverna.t2.activitiesstringconstant-activity0.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokewrite_pathway_revision_defaultValuevalue00net.sf.taverna.t2.activitiesstringconstant-activity0.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreatePathoutput_pathoutput_pathcreatePathxrefsplitLinessplitcreateFileNamepathway_namefind_pathways_by_xrefpathway_namescreateFileNamepathway_speciesfind_pathways_by_xrefpathway_speciescreateFileNamepath_nameclone_listclonescountlistfind_pathways_by_xrefpathway_namessplitLinesstringreadXrefListfilecontentssplitLinesregexsplitLines_regex_defaultValuevaluereadXrefListfileurlxreflistclone_listcopy_numbercountcountclone_listinputcreatePathpath_namefind_pathways_by_xrefsystem_codefind_pathways_by_xref_system_code_defaultValuevaluefind_pathways_by_xrefidentifiersplitLinessplitwrite_pathwayfile_typefile_typewrite_pathwayfile_namecreateFileNamefile_namewrite_pathwaypathway_idfind_pathways_by_xrefpathway_idswrite_pathwayrevisionwrite_pathway_revision_defaultValuevaluewritten_fileswrite_pathwaywrittenFile Thomas Kelder 2009-02-02 16:58:14.366 CET Download pathways for external references list 2009-02-02 16:58:14.366 CET Takes a list of external references to genes/proteins/metabolites, finds all pathways on WikiPathways that contain one of the given genes/proteins/metabolites and downloads them in a given file format. 2009-02-02 16:58:14.366 CET CloneItemsInListcopy_number00input00clonesCloneinput0copy_number0clones11net.sf.taverna.t2.activitiesbeanshell-activity0.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true copy_number 0 'text/plain' java.lang.String true input 0 'text/plain' 1 clones 1 'text/plain' net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeCloneinputinputClonecopy_numbercopy_numberclonesCloneclones Utility workflow that clones an item copy_number times. You can use this to work around standard iteration strategies, e.g. in combination with the CountListItems workflow. Workflow examples: TestIterationStrategy_withClones. For an alternative approach see TestIterationStrategy_withNesting. Example I/O: input: A copy_number: 3 result: [A,A,A] input: [A,B,C] copy_number: 3 result: [[A,A,A][B,B,B][C,C,C]] input: [A,B,C] copy_number: [3,2] result: [[[A,A,A],[A,A]][[B,B,B],[B,B]],[[C,C,C],[C,C]]] input: [A,B,C] copy_number: [3,2,1] iteration strategy: dot product result: [[A,A,A],[B,B],[C]] 2009-02-02 16:58:14.263 CET CloneItemsInList 2009-02-02 16:58:14.263 CET Marco Roos (AID) 2009-02-02 16:58:14.263 CET Getpathwaysbyexternalreferenceidentifier00system_code00pathway_namespathway_speciespathway_idsgetIdxpath0xml-text0nodelistAsXML11nodelist11net.sf.taverna.t2.activitieslocalworker-activity0.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity dom4j:dom4j:1.6 workflow dom4j dom4j 1.6 java.lang.String true xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' 1 nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSpeciesxpath0xml-text0nodelist11nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity0.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity dom4j:dom4j:1.6 workflow dom4j dom4j 1.6 java.lang.String true xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' 1 nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefindPathwaysByXrefInputcode0id0output00net.sf.taverna.t2.activitieswsdl-activity0.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="findPathwaysByXref" name="parameters" qname="{http://www.wso2.org/php/xsd}findPathwaysByXref"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="id" qname="{http://www.wso2.org/php/xsd}&gt;findPathwaysByXref&gt;id" /><s:basetype optional="false" unbounded="false" typename="string" name="code" qname="{http://www.wso2.org/php/xsd}&gt;findPathwaysByXref&gt;code" /></s:elements></s:complextype></s:extensions> java.lang.String true id 0 'text/plain' java.lang.String true code 0 'text/plain' 0 output 0 'text/xml' net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetNamesxml-text0xpath0nodelist11nodelistAsXML11net.sf.taverna.t2.activitieslocalworker-activity0.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity dom4j:dom4j:1.6 workflow dom4j dom4j 1.6 java.lang.String true xpath 0 'text/plain' java.lang.String true xml-text 0 'text/xml' 1 nodelist 1 l('text/plain') 1 nodelistAsXML 1 l('text/plain') net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefindPathwaysByXrefparameters0parameters00attachmentList11net.sf.taverna.t2.activitieswsdl-activity0.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.wikipathways.org/wpi/webservice/webservice.php?wsdl findPathwaysByXref net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetId_xpath_defaultValuevalue00net.sf.taverna.t2.activitiesstringconstant-activity0.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity //*[local-name()="id"] net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSpecies_xpath_defaultValuevalue00net.sf.taverna.t2.activitiesstringconstant-activity0.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity //*[local-name()="species"] net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetNames_xpath_defaultValuevalue00net.sf.taverna.t2.activitiesstringconstant-activity0.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity //*[local-name()="result"]/*[local-name()="name"] net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetIdxpathgetId_xpath_defaultValuevaluegetIdxml-textfindPathwaysByXrefparametersgetSpeciesxpathgetSpecies_xpath_defaultValuevaluegetSpeciesxml-textfindPathwaysByXrefparametersfindPathwaysByXrefInputcodesystem_codefindPathwaysByXrefInputididentifiergetNamesxml-textfindPathwaysByXrefparametersgetNamesxpathgetNames_xpath_defaultValuevaluefindPathwaysByXrefparametersfindPathwaysByXrefInputoutputpathway_namesgetNamesnodelistpathway_speciesgetSpeciesnodelistpathway_idsgetIdnodelist Finds pathways on WikiPathways by an external gene/protein/metabolite reference. See http://www.pathvisio.org/Help_1.1#Supported_database_systems for a list of supported database systems. 2009-02-02 16:58:14.335 CET Get pathways by external reference 2009-02-02 16:58:14.335 CET Thomas Kelder 2009-02-02 16:58:14.335 CET Writepathwaytodiskfile_type00revision00file_name00pathway_id00writtenFileconcat_filetypestring20string10output00net.sf.taverna.t2.activitieslocalworker-activity0.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow java.lang.String true string1 0 'text/plain' java.lang.String true string2 0 'text/plain' 0 output 0 'text/plain' net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeconcat_dotstring20string10output00net.sf.taverna.t2.activitieslocalworker-activity0.4net.sf.taverna.t2.activities.localworker.LocalworkerActivity workflow java.lang.String true string1 0 'text/plain' java.lang.String true string2 0 'text/plain' 0 output 0 'text/plain' net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokewriteFilefileName0data0net.sf.taverna.t2.activitiesbeanshell-activity0.4net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true data 0 'text/plain' java.lang.String true fileName 0 'text/plain' net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetPathwayAs_inputpwId0fileType0revision0output00net.sf.taverna.t2.activitieswsdl-activity0.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getPathwayAs" name="parameters" qname="{http://www.wso2.org/php/xsd}getPathwayAs"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="fileType" qname="{http://www.wso2.org/php/xsd}&gt;getPathwayAs&gt;fileType" /><s:basetype optional="false" unbounded="false" typename="string" name="pwId" qname="{http://www.wso2.org/php/xsd}&gt;getPathwayAs&gt;pwId" /><s:basetype optional="false" unbounded="false" typename="int" name="revision" qname="{http://www.wso2.org/php/xsd}&gt;getPathwayAs&gt;revision" /></s:elements></s:complextype></s:extensions> java.lang.String true fileType 0 'text/plain' java.lang.String true pwId 0 'text/plain' java.lang.String true revision 0 'text/plain' 0 output 0 'text/xml' net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetPathwayAsOutputinput0data00net.sf.taverna.t2.activitieswsdl-activity0.4net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity <s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="getPathwayAsResponse" name="parameters" qname="{http://www.wso2.org/php/xsd}getPathwayAsResponse"><s:elements><s:basetype optional="false" unbounded="false" typename="base64Binary" name="data" qname="{http://www.wso2.org/php/xsd}&gt;getPathwayAsResponse&gt;data" /></s:elements></s:complextype></s:extensions> java.lang.String true input 0 'text/xml' 0 data 0 'application/octet-stream' net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetPathwayAsparameters0attachmentList11parameters00net.sf.taverna.t2.activitieswsdl-activity0.4net.sf.taverna.t2.activities.wsdl.WSDLActivity http://www.wikipathways.org/wpi/webservice/webservice.php?wsdl getPathwayAs net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeconcat_dot_string2_defaultValuevalue00net.sf.taverna.t2.activitiesstringconstant-activity0.4net.sf.taverna.t2.activities.stringconstant.StringConstantActivity . net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 0 0 0 net.sf.taverna.t2workflowmodel-impl0.4net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeconcat_filetypestring2file_typeconcat_filetypestring1concat_dotoutputconcat_dotstring2concat_dot_string2_defaultValuevalueconcat_dotstring1file_namewriteFilefileNameconcat_filetypeoutputwriteFiledatagetPathwayAsOutputdatagetPathwayAs_inputpwIdpathway_idgetPathwayAs_inputfileTypefile_typegetPathwayAs_inputrevisionrevisiongetPathwayAsOutputinputgetPathwayAsparametersgetPathwayAsparametersgetPathwayAs_inputoutputwrittenFileconcat_filetypeoutput Thomas Kelder 2009-02-02 16:58:14.365 CET Write pathway to disk 2009-02-02 16:58:14.365 CET Downloads and writes a pathway from WikiPathways to a local disk in the given file type. 2009-02-02 16:58:14.365 CET